Browsing by Subject "Protein"

Now showing 1 - 16 of 16

Open Access
Atomic force microscopy for the investigation of molecular and cellular behavior
(Elsevier, 2016-10) Ozkan A.D.; Topal, A. E.; Dana, A.; Güler, Mustafa O.; Tekinay, A. B.
The present review details the methods used for the measurement of cells and their exudates using atomic force microscopy (AFM) and outlines the general conclusions drawn by the mechanical characterization of biological materials through this method. AFM is a material characterization technique that can be operated in liquid conditions, allowing its use for the investigation of the mechanical properties of biological materials in their native environments. AFM has been used for the mechanical investigation of proteins, nucleic acids, biofilms, secretions, membrane bilayers, tissues and bacterial or eukaryotic cells; however, comparison between studies is difficult due to variances between tip sizes and morphologies, sample fixation and immobilization strategies, conditions of measurement and the mechanical parameters used for the quantification of biomaterial response. Although standard protocols for the AFM investigation of biological materials are limited and minor differences in measurement conditions may create large discrepancies, the method is nonetheless highly effective for comparatively evaluating the mechanical integrity of biomaterials and can be used for the real-time acquisition of elasticity data following the introduction of a chemical or mechanical stimulus. While it is currently of limited diagnostic value, the technique is also useful for basic research in cancer biology and the characterization of disease progression and wound healing processes.
Open Access
Chromatin-modifying enzymes as modulators of reprogramming
(Nature Publishing Group, 2012) Onder, T. T.; Kara, N.; Cherry, A.; Sinha, A. U.; Zhu, N.; Bernt, K. M.; Cahan, P.; Marcarci, B. O.; Unternaehrer, J.; Gupta, P. B.; Lander, E. S.; Armstrong, S. A.; Daley, G. Q.
Generation of induced pluripotent stem cells (iPSCs) by somatic cell reprogramming involves global epigenetic remodelling. Whereas several proteins are known to regulate chromatin marks associated with the distinct epigenetic states of cells before and after reprogramming, the role of specific chromatin-modifying enzymes in reprogramming remains to be determined. To address how chromatin-modifying proteins influence reprogramming, we used short hairpin RNAs (shRNAs) to target genes in DNA and histone methylation pathways, and identified positive and negative modulators of iPSC generation. Whereas inhibition of the core components of the polycomb repressive complex 1 and 2, including the histone 3 lysine 27 methyltransferase EZH2, reduced reprogramming efficiency, suppression of SUV39H1, YY1 and DOT1L enhanced reprogramming. Specifically, inhibition of the H3K79 histone methyltransferase DOT1L by shRNA or a small molecule accelerated reprogramming, significantly increased the yield of iPSC colonies, and substituted for KLF4 and c-Myc (also known as MYC). Inhibition of DOT1L early in the reprogramming process is associated with a marked increase in two alternative factors, NANOG and LIN28, which play essential functional roles in the enhancement of reprogramming. Genome-wide analysis of H3K79me2 distribution revealed that fibroblast-specific genes associated with the epithelial to mesenchymal transition lose H3K79me2 in the initial phases of reprogramming. DOT1L inhibition facilitates the loss of this mark from genes that are fated to be repressed in the pluripotent state. These findings implicate specific chromatin-modifying enzymes as barriers to or facilitators of reprogramming, and demonstrate how modulation of chromatin-modifying enzymes can be exploited to more efficiently generate iPSCs with fewer exogenous transcription factors. © 2012 Macmillan Publishers Limited. All rights reserved.
Open Access
Comparative analysis of the domestic cat genome reveals genetic signatures underlying feline biology and domestication
(Proceedings of the National Academy of Sciences, 2014-12-02) Montague, M. J.; Li, G.; Gandolfi, B.; Khan, R.; Aken, B. L.; Marques Bonet, T.; Alkan C.; Thomas, G. W. C.; Warren, W. C.; Searle, S. M. J.; Minx, M.; Hilliera, LaDeana W.; Koboldt, D. C.; Davis, B. W.; Driscoll, C. A.; Barr, C. S.; Blackistone, K.; Quilez, J.; Lorente-Galdos, B.; Marques Bonet, T.; Hahnj, M. W.; Menotti-Raymond, M.; O’Brien, S. J.; Wilson, R. K.; Lyons, L. A.; Murphy, W. J.
Little is known about the genetic changes that distinguish domestic cat populations from their wild progenitors. Here we describe a high-quality domestic cat reference genome assembly and comparative inferences made with other cat breeds, wildcats, and other mammals. Based upon these comparisons, we identified positively selected genes enriched for genes involved in lipid metabolism that underpin adaptations to a hypercarnivorous diet. We also found positive selection signals within genes underlying sensory processes, especially those affecting vision and hearing in the carnivore lineage. We observed an evolutionary tradeoff between functional olfactory and vomeronasal receptor gene repertoires in the cat and dog genomes, with an expansion of the feline chemosensory system for detecting pheromones at the expense of odorant detection. Genomic regions harboring signatures of natural selection that distinguish domestic cats from their wild congeners are enriched in neural crest-related genes associated with behavior and reward in mouse models, as predicted by the domestication syndrome hypothesis. Our description of a previously unidentified allele for the gloving pigmentation pattern found in the Birman breed supports the hypothesis that cat breeds experienced strong selection on specific mutations drawn from random bred populations. Collectively, these findings provide insight into how the process of domestication altered the ancestral wildcat genome and build a resource for future disease mapping and phylogenomic studies across all members of the Felidae.
Open Access
Design and construction of protein and peptide-based self-assembled nanostructures
(Elsevier, 2022-01-01) Yuca, Esra; Khan, Anooshay; Hacıosmanoğlu, Nedim; Şeker, Urartu Özgür Şafak; Pandya, A.; Singh, V.; Bhosale, R. S.
Self-assembly is the driving force for the formation of biological materials. From nucleic acid conformations to more complex cellular organizations, self-assembling structures shape biological functionality. So, the design of self-assembling biomolecular structures holds a great advantage for enhanced material properties. In biological processes, inorganic structures are created in a hierarchical fashion utilizing biomolecule-based templates. Since they have recognition and self-assembly properties, biomolecules can control highly organized inorganic material formation in nature. The bio-templating approach takes advantage of biomolecules’ self-assembly properties to develop new nanostructures with superior chemical and physical properties. Here, peptides and proteins including β-sheets, β-hairpins, α-helix, amyloid, capsid, ferritin, and albumin, used in the formation of nanostructures with desired functionality under mild environmental conditions, and their applications are discussed.
Open Access
Differential expression patterns of metastasis suppressor proteins in basal cell carcinoma
(Wiley-Blackwell Publishing Ltd., 2015) Bozdogan, O.; Yulug, I. G.; Vargel, I.; Cavusoglu, T.; Karabulut, A. A.; Karahan, G.; Sayar, N.
Background: Basal cell carcinomas (BCCs) are common malignant skin tumors. Despite having a significant invasion capacity, they metastasize only rarely. Our aim in this study was to detect the expression patterns of the NM23-H1, NDRG1, E-cadherin, RHOGDI2, CD82/KAI1, MKK4, and AKAP12 metastasis suppressor proteins in BCCs. Methods: A total of 96 BCC and 10 normal skin samples were included for the immunohistochemical study. Eleven frozen BCC samples were also studied by quantitative real time polymerase chain reaction (qRT-PCR) to detect the gene expression profile. Results: NM23-H1 was strongly and diffusely expressed in all types of BCC. Significant cytoplasmic expression of NDRG1 and E-cadherin was also detected. However, AKAP12 and CD82/KAI1 expression was significantly decreased. The expressions of the other proteins were somewhere between the two extremes. Similarly, qRT-PCR analysis showed down-regulation of AKAP12 and up-regulation of NM23-H1 and NDRG1 in BCC. Morphologically aggressive BCCs showed significantly higher cytoplasmic NDRG1 expression scores and lower CD82/KAI1 scores than non-aggressive BCCs. Conclusion: The relatively preserved levels of NM23-H1, NDRG1, and E-cadherin proteins may have a positive effect on the non-metastasizing features of these tumors.
Open Access
Finite size effects in cooperative molecular motors
(Elsevier B.V., 2003) Taneri, S.; Yalabik, M. C.
We have studied the ballistic and damped dynamics of finite size cooperative molecular motors. We study the effect of finite size on average quantities such as sliding velocity, as well as the statistics of fluctuations in these quantities. We observed stalling for the over damped case.
Open Access
Functionally conserved effects of rapamycin exposure on zebrafish
(Spandidos Publications, 2016-03) Sucularli, C.; Shehwana, H.; Kuscu, C.; Dungul, D. C.; Ozdag, H.; Konu, O.
Mechanistic target of rapamycin (mTOR) is a conserved serine/threonine kinase important in cell proliferation, growth and protein translation. Rapamycin, a well-known anti-cancer agent and immunosuppressant drug, inhibits mTOR activity in different taxa including zebrafish. In the present study, the effect of rapamycin exposure on the transcriptome of a zebrafish fibroblast cell line, ZF4, was investigated. Microarray analysis demonstrated that rapamycin treatment modulated a large set of genes with varying functions including protein synthesis, assembly of mitochondrial and proteasomal machinery, cell cycle, metabolism and oxidative phosphorylation in ZF4 cells. A mild however, coordinated reduction in the expression of proteasomal and mitochondrial ribosomal subunits was detected, while the expression of numerous ribosomal subunits increased. Meta-analysis of heterogeneous mouse rapamycin microarray datasets enabled the comparison of zebrafish and mouse pathways modulated by rapamycin, using Kyoto Encyclopedia of Genes and Genomes and Gene Ontology pathway analysis. The analyses demonstrated a high degree of functional conservation between zebrafish and mice in response to rapamycin. In addition, rapamycin treatment resulted in a marked dose-dependent reduction in body size and pigmentation in zebrafish embryos. The present study is the first, to the best of our knowledge, to evaluate the conservation of rapamycin-modulated functional pathways between zebrafish and mice, in addition to the dose-dependent growth curves of zebrafish embryos upon rapamycin exposure.
Open Access
Genetic analysis of MEFV gene pyrin domain in patients with Behçet's disease
(Hindawi Publishing Corporation, 2006) Dursun, A.; Durakbasi-Dursun, H. G.; Zamani, A. G.; Gulbahar, Z. G.; Dursun, R.; Yakicier, C.
Objectives. Behçet's disease (BD) is a systemic vasculitis with recurrent oral and genital ulcers and uveitis. MEFV gene, which is the main factor in familial Mediterranean fever (FMF), is also reported to be a susceptibility gene for BD. The pyrin domain of MEFV gene is a member of death-domain superfamily and has been proposed to regulate inflammatory signaling in myeloid cells. This study was designed to determine if mutations in pyrin domain of MEFV gene are involved in BD. Methods. We analyzed the pyrin domain of MEFV gene in 54 Turkish patients with BD by PCR-analysis and direct sequencing. Results. Neither deletion or insertion mutations nor point mutations in pyrin domain were found in any patient. Conclusion. Although pyrin gene mutations have been reported in patients with BD, pyrin domain is not mutated. However, alterations in other regions of MEFV gene and interaction between pyrin domains are needed to be further investigated. Copyright © 2006 Ahmet Dursun et al.
Open Access
Identification of relative protein bands in polyacrylamide gel electrophoresis (PAGE) using a multi-resolution snake algorithm
(Informa Healthcare, 1999-06) Gürcan, M. N.; Koyutürk, M.; Yildiz, H. S.; Çetin-Atalay R.; Çetin, A. Enis
In polyacrylamide gel electrophoresis (PAGE) image analysis, it is important to determine the percentage of the protein of interest of a protein mixture. This study presents reliable computer software to determine this percentage. The region of interest containing the protein band is detected using the snake algorithm. The iterative snake algorithm is implemented in a multi-resolutional framework. The snake is initialized on a low-resolution image. Then, the final position of the snake at the low resolution is used as the initial position in the higher-resolution image. Finally, the area of the protein is estimated as the area enclosed by the final position of the snake.
Open Access
Immunization with UV-induced apoptotic cells generates monoclonal antibodies against proteins differentially expressed in hepatocellular carcinoma cell lines
(Mary Ann Liebert, Inc, 2007) Celikkaya, H.; Ciraci, C.; Oztas, E.; Avci, M. E.; Ozturk, M.; Yagci, T.
Early and differential diagnosis of hepatocellular carcinoma (HCC) requires sensitive and specific tissue and serum markers. On the other hand, proteins involved in tumorigenesis are extensively modelated on exposure to apoptotic stimuli, including ultraviolet (UVC) irradiation. Hence, we generated monoclonal antibodies by using UVC-irradiated apoptotic cells of an HCC cell line, HUH7, aiming to explore proteins differentially expressed in tumors and apoptosis. We obtained 18 hybridoma clones recognizing protein targets in apoptotic HUH7 cells, and clone 6D5 was chosen for characterization studies because of its strong reactivity in cell-ELISA assay. Subtype of the antibody was IgG3 (κ). Targets of 6D5 antibody were found to be abundantly expressed in all HCC cell lines except FLC4, which resembles normal hepatocytes. We also observed the secretion of 6D5 ligands by some of the HCC cell lines. Moreover, cellular proteins recognized by the antibody displayed a late upregulation in UVC-induced apoptotic cells. We concluded that 6D5 target proteins are modulated in liver tumorigenesis and apoptotic processes. We therefore propose the validation of our antibody in tissue and serum samples of HCC patients to assess its potential use for the early diagnosis of HCC and to understand the role of 6D5 ligands in liver carcinogenesis. © Mary Ann Liebert, Inc.
Open Access
Monitoring molecular assembly of biofilms using quartz crystal microbalance with dissipation
(Springer, 2022) Yuca, E.; Şeker, Urartu Özgür Şafak; Arluison, Véronique; Wien, Frank; Marcoleta, Andrés
The structure and the functionality of biofilm proteins, the main components of the extracellular matrix, can be tuned by protein engineering. The use of binding kinetics data has been demonstrated in the characterization of recombinantly produced biofilm proteins to control their behavior on certain surfaces or under certain conditions. Quartz crystal microbalance with dissipation monitoring (QCM-D) allows measuring the change in resonance frequency and the energy loss and distribution upon the interaction of molecules with the surface. The characterization of the molecular assembly of curli biofilm proteins on different surfaces using QCM-D is presented here as a detailed protocol. The experimental procedure detailed in this chapter can be applied and modified for other biofilm proteins or subunits to determine their surface adsorption and kinetic binding characteristics.
Open Access
Mutations in RAD21 disrupt regulation of apob in patients with chronic intestinal pseudo-obstruction
(W.B. Saunders, 2015) Bonora, E.; Bianco, F.; Cordeddu, L.; Bamshad, M.; Francescatto, L.; Dowless, D.; Stanghellini, V.; Cogliandro, R. F.; Lindberg, G.; Mungan, Z.; Cefle, K.; Ozcelik, T.; Palanduz, S.; Ozturk, S.; Gedikbasi, A.; Gori, A.; Pippucci, T.; Graziano, C.; Volta, U.; Caio, G.; Barbara, G.; D'Amato, M.; Seri, M.; Katsanis, N.; Romeo, G.; De Giorgio, R.
Background Aims Chronic intestinal pseudo-obstruction (CIPO) is characterized by severe intestinal dysmotility that mimics a mechanical subocclusion with no evidence of gut obstruction. We searched for genetic variants associated with CIPO to increase our understanding of its pathogenesis and to identify potential biomarkers. Methods We performed whole-exome sequencing of genomic DNA from patients with familial CIPO syndrome. Blood and lymphoblastoid cells were collected from patients and controls (individuals without CIPO); levels of messenger RNA (mRNA) and proteins were analyzed by quantitative reverse-transcription polymerase chain reaction, immunoblot, and mobility shift assays. Complementary DNAs were transfected into HEK293 cells. Expression of rad21 was suppressed in zebrafish embryos using a splice-blocking morpholino (rad21a). Gut tissues were collected and analyzed. Results We identified a homozygous mutation (p.622, encodes Ala>Thr) in RAD21 in patients from a consanguineous family with CIPO. Expression of RUNX1, a target of RAD21, was reduced in cells from patients with CIPO compared with controls. In zebrafish, suppression of rad21a reduced expression of runx1; this phenotype was corrected by injection of human RAD21 mRNA, but not with the mRNA from the mutated p.622 allele. rad21a Morpholino zebrafish had delayed intestinal transit and greatly reduced numbers of enteric neurons, similar to patients with CIPO. This defect was greater in zebrafish with suppressed expression of ret and rad21, indicating their interaction in the regulation of gut neurogenesis. The promoter region of APOB bound RAD21 but not RAD21 p.622 Ala>Thr; expression of wild-type RAD21 in HEK293 cells repressed expression of APOB, compared with control vector. The gut-specific isoform of APOB (APOB48) is overexpressed in sera from patients with CIPO who carry the RAD21 mutation. APOB48 also is overexpressed in sporadic CIPO in sera and gut biopsy specimens. Conclusions Some patients with CIPO carry mutations in RAD21 that disrupt the ability of its product to regulate genes such as RUNX1 and APOB. Reduced expression of rad21 in zebrafish, and dysregulation of these target genes, disrupts intestinal transit and the development of enteric neurons.
Open Access
Oligonucleotide-based label-free detection with optical microresonators: strategies and challenges
(Royal Society of Chemistry, 2016) Toren, P.; Ozgur E.; Bayındır, Mehmet
This review targets diversified oligonucleotide-based biodetection techniques, focusing on the use of microresonators of whispering gallery mode (WGM) type as optical biosensors mostly integrated with lab-on-a-chip systems. On-chip and microfluidics combined devices along with optical microresonators provide rapid, robust, reproducible and multiplexed biodetection abilities in considerably small volumes. We present a detailed overview of the studies conducted so far, including biodetection of various oligonucleotide biomarkers as well as deoxyribonucleic acids (DNAs), ribonucleic acids (RNAs) and proteins. We particularly advert to chemical surface modifications for specific and selective biosensing.
Open Access
Protein folding rates correlate with heterogeneity of folding mechanism
(American Physical Society, 2004) Öztop, B.; Ejtehadi, M. R.; Plotkin, S. S.
The folding rates of protein were shown to correlate with the degree of heterogeneity in the formation of native contacts. It was shown that both experimental rates and simulated free energy barriers for 2-state proteins depend on the degree of heterogeneity present in the folding process. Heterogeneity due to variance in the distribution of native loop lengths, and variance in the distribution of φ values, were observed to increase folding rates and reduce folding barriers. The observed effect due to φ variance was found to be the most statistically significant, because φ variance captures both heterogeneity arising from native topology and that arising from energetics.
Open Access
Regulation of Homer and group I metabotropic glutamate receptors by nicotine
(Wiley-Blackwell Publishing Ltd., 2005) Kane, J. K.; Hwang, Y.; Konu, O.; Loughlin, S. E.; Leslie, F. M.; Li, M. D.
The present study focuses on the nicotine-induced modulation of mRNA and protein expression of a number of genes involved in glutamatergic synaptic transmission in rat brain over different time periods of exposure. A subchronic (3 days) but not the chronic (7 or 14 days) administration of nicotine resulted in the up-regulation of Homer2a/b mRNA in the amygdala while in the ventral tegmental area (VTA) no change in expression of either Homer2a/b or Homer1b/c was observed. Although the increase in Homer2a/b mRNA was not translated into the protein level in the amygdala, a slight but significant up-regulation of Homer1b/c protein was observed in the same region at day 3. Both Homer forms were up-regulated at the protein level in the VTA at day 3. In the nucleus accumbens, 14 days of nicotine treatment up-regulated mRNA of Homer2b/c by 68.2% (P < 0.05), while the short form Homer1a gene was down-regulated by 65.0% at day 3 (P < 0.05). In regard to other components of the glutamatergic signalling, we identified an acute and intermittent increase in the mRNA and protein levels of mGluR1 and mGluR5 in the amygdala. In the VTA, however, the effects of nicotine on mGluR mRNA expression were long-lasting but rather specific to mGluR1. Nevertheless, mGluR1 protein levels in the VTA area were up-regulated only at day 3, as in the amygdala. These data provide further evidence for the involvement of nicotine in the glutamatergic neuronal synaptic activity in vivo, suggesting a role for the newly identified Homer proteins in this paradigm.
Open Access
Two learning approaches for protein name extraction
(Academic Press, 2009) Tatar, S.; Cicekli, I.
Protein name extraction, one of the basic tasks in automatic extraction of information from biological texts, remains challenging. In this paper, we explore the use of two different machine learning techniques and present the results of the conducted experiments. In the first method, Bigram language model is used to extract protein names. In the latter, we use an automatic rule learning method that can identify protein names located in the biological texts. In both cases, we generalize protein names by using hierarchically categorized syntactic token types. We conducted our experiments on two different datasets. Our first method based on Bigram language model achieved an F-score of 67.7% on the YAPEX dataset and 66.8% on the GENIA corpus. The developed rule learning method obtained 61.8% F-score value on the YAPEX dataset and 61.0% on the GENIA corpus. The results of the comparative experiments demonstrate that both techniques are applicable to the task of automatic protein name extraction, a prerequisite for the large-scale processing of biomedical literature. © 2009 Elsevier Inc. All rights reserved.